Microbial communities play crucial roles in marine ecosystem functioning and biogeochemical cycles, and this is also the case for coral reefs. Coral holobionts, the keystone architects of the coral reef ecosystem, comprise notorious associations between an invertebrate host and both eukaryotic and prokaryotic microbes. These provide crucial services to the coral host, covering its nutritional and immunity needs, and therefore contributing to its ecological dominance in tropical shallow oligotrophic waters. Here we focus on several case studies implicating host-microbial associations within the coral holobiont, aiming to illustrate the degree of integration and interdependence established between corals and their symbionts. At the interface between the host epithelium and the seawater environment, coral surface mucus supports a microbial community that acts as barrier against a wide range of pathogens. Our findings suggest a selective role of mucus carbohydrate fractionation in the response of the associated prokaryotic community. This mechanism can potentially explain the observed host-specificity of ectosymbiotic microbial communities associated with coral mucus. We also show that the fate of the coral holobiont upon external disturbance relates to the degree of disruption of its mucus microbial community, with recovery being dependent on the persistence of an intact beneficial microbiome, in contrast to stochastic successions leading to the dominance of pathogens and host death. This finding supports the view that the natural prokaryotic community inhabiting coral mucus is a key component of the coral holobiont and that there are deterministic relationships between microbial successions and host health. Finally, we explore the biochemical variation and the dynamic response of microbial communities inhabiting the gastrovascular cavity of corals upon feeding activities of the host to elucidate on the fairly unexplored microbial ecology of this semi-closed environment. By jointly presenting this series of recent findings on microbial successions within coral hosts we highlight the complexity of symbiotic interactions established within the coral holobiont and illustrate how determinant these interactions are for coral health.